I've only used Calibre to put ebooks onto my Kindle 3 so far, and it hasn't been connected to wi-fi. I scanned it the other day and it showed up with joiiruw.exe, x.exe and ert.dll.
My anti-virus has deleted those files from the device, but now I'm not able to see any of my files by just going through My Computer. Calibre still shows all of the ebooks on the device. Using Calibre to switch more ebooks onto the device hasn't shown any other viruses, but I was wondering if anyone else has had this problem?

Also, is there a way to fix it so I can see the files through My Computer again? I'm thinking maybe just to do a reset to factory default.

I've only used Calibre to put ebooks onto my Kindle 3 so far, and it hasn't been connected to wi-fi. I scanned it the other day and it showed up with joiiruw.exe, x.exe and ert.dll.
My anti-virus has deleted those files from the device, but now I'm not able to see any of my files by just going through My Computer. Calibre still shows all of the ebooks on the device. Using Calibre to switch more ebooks onto the device hasn't shown any other viruses, but I was wondering if anyone else has had this problem?

Also, is there a way to fix it so I can see the files through My Computer again? I'm thinking maybe just to do a reset to factory default.

Any ideas?
Thanks.

Calibre only copies book files to your device, so if they were there, something put them there.
Note,: It is possible to imbed executable's into RAR and ZIP and EPUB.
The source of those files should be blacklisted if you ever find an infection

Calibre ships uninfected from the two main download sites (Sourceforge and Google Code, the latter one is the download you get from calibre-ebook.com). If you got it there, it could have been infected after being installed on your PC. Don't download from other download pages, as there's no guarantee what you'll get.